Since Ubuntu 12.04 upgrade, the Thunderbird scrollbar position were not visible any more. The scrollbar works but you have no visual feedback to know where you are in your long lists. Annoying!!! It turns out that this was a feature of the overlay scrollbar.

To restore the Thunderbird scrollbar, remove the following packages which are causing these troubles:

sudo apt-get remove overlay-scrollbar liboverlay-scrollbar-0.2-0 liboverlay-scrollbar3-0.2-0

Since I've disabled it, I realized many others have the issue. The How do I disable overlay scrollbars? Q&A gives other hints.